Interpretive Summary: Bacteria and other microbes inhabit many sites in the human body. Recently, there is renewed interest in learning about the contributions of these microbes and their relationship to maintaining human health. Based on current knowledge, the microbiota in the intestinal tract is the most complex with respect to the total numbers of bacteria, their interaction with the mucosal immune system, and their contribution to various functions of the host’s physiology. The large intestine supports a diverse microbiota that ferments complex substrates such as dietary fiber and host mucins, and also metabolizes bile acids and phytoestrogens that reach the large intestine. It is now well established that microbiota composition not only differs between individuals but over time within individuals. However, a thorough understanding of the sources of variations in microbiota composition is lacking. Microbiota composition varies depending on the type of sample collected (stool samples, stool swabs or superficial rectal or intestinal biopsies), and the time of collection. Microbiota dynamics are affected by life style factors including diet and exercise that determine what nutrients reach the proximal colon and how fast these nutrients pass through. Based on samples from nutritional intervention studies, we review sample collection methods for gut microbiota studies, and explore recent findings about the dynamics of microbiota composition. Finally, we recommend standardizing human microbiota analysis to facilitate comparison and potentially pooling between studies. This information is important to scientists working to explore the relationships between these complex ecosystems and their effect of host health.

Technical Abstract:
Humans harbor distinct commensal microbiota at various anatomic sites. There has been renewed interest in the contributions of microbiota activities to human health and disease. The microbiota of the gut is the most complex of all anatomic sites in terms of total numbers of bacteria that interact closely with the mucosal immune system and contribute various functions to host physiology. Especially in the proximal large intestine a diverse microbiota ferments complex substrates such as dietary fiber and host mucins, but also metabolizes bile acids and phytoestrogens that reach the large intestine. It is now well established that microbiota composition differs between but over time also within individuals. However, a thorough understanding of the sources of variations in microbiota composition, which is an important requirement for large population based microbiota studies is lacking. Microbiota composition varies depending on what kind of sample is collected, most commonly stool samples, stool swabs or superficial rectal or intestinal biopsies, and the time of collection. Microbiota dynamics are affected by life style factors including diet and exercise that determine what nutrients reach the proximal colon and how fast these nutrients pass through (transit time). Here we review sample collection issues in gut microbiota studies and recent findings about dynamics in microbiota composition. Finally, we recommend standardizing human microbiota analysis to facilitate comparison and potentially pooling between studies.